Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants

Li, Wei; Liu, Wei; Wei, Hengling; He, Qiuling; Chen, Jinhong; Zhang, Baohong; Zhu, Shuijin

doi:10.1371/journal.pone.0094172

Cited by 42 publications

(49 citation statements)

References 58 publications

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“…We found 15 white spruce HMG‐R genes, including five putative pseudogenes. The number in other plant genomes ranges from one in Selaginella moellendorffii to nine in Gossypium raimondii (Li et al ., ). All but one of the white spruce HMG‐Rs clustered distinctly between the angiosperm and lower plant clades, while one appeared at the base of the angiosperm clade (Figure S8).…”

Section: Discussionmentioning

confidence: 97%

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Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

et al. 2015

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These authors contributed equally to this work. SUMMARYWhite spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

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Section: Discussionmentioning

confidence: 97%

“…Li et al . () described an expansion of HMG‐R genes in plants, not including a sequenced gymnosperm genome. We found 15 white spruce HMG‐R genes, including five putative pseudogenes.…”

Section: Discussionmentioning

confidence: 99%

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

et al. 2015

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“…This study also analyzed the genes based on RNA-seq and gene-to-metabolites correlation. The number of HMGR genes varies from plant to plant [38]. There are two HMGR genes reported in Panax ginseng 'Meyer' plant, which are PgHMGR1 and PgHMGR2 [39].…”

Section: Gene-to-metabolites Correlation Analysismentioning

confidence: 99%

Genome-wide transcriptome analysis of triterpene biosynthetic genes of Anoectochilus roxburghii plant

Wang¹,

Xu²,

Brodelius³

et al. 2020

Preprint

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Background: Anoectochilus roxburghii is a medicinal plant and contains a variety of bioactive components, including triterpene, which exhibits important pharmacological properties with low toxicity. However, little is known about the biosynthetic pathway of triterpene or about the genome and transcriptome in A. roxburghii. Results: In order to analyze transcriptional determinants related to the biosynthesis of the bioactive components, we performed transcriptome sequencing in A. roxburghii (SRX1818644, SRX1818642 and SRX1818641) and annotated the sequences from three samples. In total, 137,679,059 clean reads were obtained, corresponding to 12.20 Gb of total nucleotides. They were then assembled into 86,382 contigs and 68,938 unigenes, which were further annotated according to sequence similarity with known genes in COG, EST, Nr, Pfam and Uniprot databases, leading to 10,040，29,442，39,551，34,991 and 28,082 unigenes, respectively. GO analysis classified all unigenes into three functional categories, i.e. biological processes (43,206 unigenes in 22 categories), molecular functions (46,978 unigenes in 15 categories) and cellular components (20,951 unigenes in 18 categories). Candidate triterpenes biosynthetic genes ArHMGR1 in MEV pathway, ArDXS1, ArDXS4 ArDXS5, ArDXS8-10, ArDXR1-2 and ArHDR1-2 in MEP pathway and ArFDS1, ArSM and ArOCS were selected based on RNA-seq and gene-to-metabolites correlation analysis. Conclusion: The transcriptomes of A. roxburghii plant include 86,382 contigs and 68,938 unigenes. The assembled dataset allowed identification of genes encoding enzymes in the biosynthesis of bioactive components in A. roxburghii plant. Candidate genes that encode enzymes being important in triterpenes biosynthetic pathway were selected. This will facilitate the study of expression and regulation in the biosynthesis of bioactive component in A.roxburghii.

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“…The mammalian genome and that of the fission yeast Schizosaccharomyces pombe contain only one gene encoding HMGR, whereas the genome of the budding yeast Saccharomyces cerevisiae harbors two isozymes, and in all plant species studied so far, HMGR is encoded by a multigene family [26,[61][62][63][64][65][66].…”

Section: Posttranslational Regulation Of Enzyme Stability Of the Terpmentioning

confidence: 99%

Review: Endoplasmic Reticulum-Associated Degradation (ERAD)-Dependent Control of (Tri)terpenoid Metabolism in Plants

Erffelinck

Goossens

2018

Planta Med

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Plants are sessile organisms. Therefore, they developed the capacity to quickly respond to biotic and abiotic environmental stresses, for instance by producing a broad spectrum of bioactive specialized metabolites. In this defense response, the jasmonate phytohormones can instigate a signaling cascade that leads to the specific elicitation and reprograming of numerous metabolic pathways. Recent research progress has provided several insights into the regulatory networks of many specialized metabolic pathways, mainly at the transcriptional level. Nonetheless, our view on the regulation of defense metabolism remains far from comprehensive. Here, we describe the recent advances obtained with regard to one aspect of the regulation of plant specialized metabolism, namely the posttranslational regulation of enzyme stability. We focus on terpenoid biosynthesis and in particular on the rate-limiting and well-investigated enzyme of the terpenoid precursor pathway, 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR). There are clear similarities, as well as important mechanistic differences, among the components involved in the posttranslational regulation of terpenoid biosynthesis via HMGR in plants, yeasts, and mammals. Furthermore, in plants, several of these components evolved to respond to specific signaling cues. Indeed, the elements of the plant endoplasmic reticulum-associated degradation (ERAD) and ER stress-associated processes can be induced upon environmental stresses and during specific developmental processes, thereby allowing a unique posttranslational regulation of terpenoid biosynthesis pathways.

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Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants

Cited by 42 publications

References 58 publications

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

Genome-wide transcriptome analysis of triterpene biosynthetic genes of Anoectochilus roxburghii plant

Review: Endoplasmic Reticulum-Associated Degradation (ERAD)-Dependent Control of (Tri)terpenoid Metabolism in Plants

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